Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen in the U.S. with an annual incidence of 5 million cases. Studies have been in progress to define the clinical spectrum of chlamydial infection, to develop improved diagnostic assays and to examine its pathogenesis. In screening 19,000 patients attending various Baltimore clinics, we have demonstrated that molecular amplification assays, including polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA), have markedly improved the sensitivity of detection of C. trachomatis. The prevalence of chlamydia infection determined by screening urine samples by PCR was 13% among women attending STD clinics, 7% in family planning clinics, and 11% in adolescent high school clinics. These data were geomapped for Baltimore which demonstrated two geographically distinct cores for gonorrhea with a rate greater than 5700/100,000, whereas chlamydia could not be mapped to any specific cores. We utilized the advantages of urine-based LCR to screen 2,000 female military recruits and found the prevalence for C. trachomatis to be 6.7%; positivity correlated with age less than 25, African-American ethnicity, and a new sexual partner. In a multi-country trial examining the efficacy of oral azithromycin in the treatment of trachoma, the ocular chlamydia infection rate dropped from 50% to 2% following azithromycin compared to 19% following tetracycline topical treatment. We demonstrated that trachoma is associated with a pro-inflammatory cytokine profile (expression of IL-1beta, IL-6, and TNF-alpha mRNA), and favored a CMI response (IL-2, IL-12, and IFN-gamma present). Following our development of a PCR assay for C. pneumoniae, we identified C. pneumoniae in 8% of 700 patients with respiratory disease. In vitro studies have demonstrated replication of C. pneumoniae in human pulmonary macrophages, pulmonary artery endothelial cells, and aortic artery endothelial and smooth muscle cells. After screening 50 individuals with severe coronary atherosclerosis, we have demonstrated by culture, PCR, electron microscopy, and in situ hybridization, the presence of C. trachomatis in coronary atheromas in six patients. Additional studies are planned to further address the role of C. pneumoniae in respiratory disease and atherosclerotic heart disease.